-
Notifications
You must be signed in to change notification settings - Fork 147
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
v.maxent.swd: update manual page, added option to thin point layers a…
…nd bugfixes (#1022) - Included an example - Added option to thin species presence and background point layers. - Bug fixes Co-authored-by: Markus Neteler <neteler@osgeo.org>
- Loading branch information
Showing
2 changed files
with
188 additions
and
79 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,97 +1,159 @@ | ||
| <h2>DESCRIPTION</h2> | ||
|
|
||
| <em>v.maxent.swd</em> Produce a set of SWD files as input to MaxEnt | ||
| 3.3.3k+, based on a point vector layer(s) of species distribution(s), a | ||
| point layer with background points and user-defined raster layers. The | ||
| user can also let the function create the background point file. | ||
| (respecting region and mask, if set). | ||
| The <em>v.maxent.swd</em> takes one or more point vector layers with | ||
| the location of species presence locations (parameter: <b>species</b>), | ||
| and a set of raster layers representing relevant environmental | ||
| variables (parameter: <b>evp_maps</b>). For all point locations, it | ||
| reads in the values of the environmental raster layers. The resulting | ||
| point layers(s) are combined in one layer and this is exported as a SWD | ||
| file that can be used as input for MaxEnd 3.4 or higher. | ||
|
|
||
| <p> | ||
| The SWD file format is a simple CSV-like file format as described | ||
| in Elith et al. 2011. The first three fields provide the species name, | ||
| x-coordinate and y-coordinate, while subsequent fields contain the | ||
| values of the user-selected environmental parameters. Note that the | ||
| coordinates are not used by the MaxEnt program if all environmental | ||
| data is given in the SWD format file. | ||
|
|
||
| <p> | ||
| The user can provide one or more species point files, which will be | ||
| combined in one SWD file. The map names of both the species point | ||
| layers and the environmental parameters can be replaced by alias names, | ||
| which will be used by MaxEnt. | ||
| The user can also provide a point layer with background points | ||
| (parameter: <b>bgp</b>). Alternatively, a user-defined number of | ||
| background points can be generated automatically, respecting the | ||
| computational region and MASK. In either case, for all point locations, | ||
| the function reads in the values of the environmental raster layers. | ||
| The resulting point layer is exported as a SWD file. | ||
|
|
||
| <p> | ||
| If alias names are used, a CSV file (alias_file) can be created with | ||
| alias names in the first column and map names in the second column, | ||
| separated by comma, without header. This can be used as input in | ||
| r.maxent.lambdas (but note that this addon does not seem to work with | ||
| outputs from Maxent 3.4+). | ||
| separated by comma, without a header. | ||
|
|
||
| <h2>NOTES</h2> | ||
|
|
||
| The SWD output files are simple comma delimited text | ||
| files (.csv) and can therefore be easily read in in for example R | ||
| and subsequently used in other models / functions. | ||
| The map names of both the species point layers and the environmental | ||
| parameters can be replaced by alias names, which will be used by | ||
| MaxEnt. | ||
|
|
||
| <p> | ||
| Maxent expects the raster cells to be perfectly square. I.e., the n-s | ||
| and e-w resolution need to be the same. v.maxent.swd will fail if this | ||
| is not the case. If this happens, you should change the resolution. | ||
| The SWD file format is a simple comma-delimited text files. The first | ||
| three fields provide the species name, x-coordinate and y-coordinate, | ||
| while subsequent fields contain the values of the user-selected | ||
| environmental parameters. The files can be easily read in for example, | ||
| R and subsequently used in other models / functions. | ||
|
|
||
| <p> | ||
| Following the grass gis convention, the resolution of an exported | ||
| raster is determined by the region settings. So make sure to set the | ||
| resolution of the region so that the n-s and e-w resolution match. To | ||
| accomplish this, you can use (replaced the *** for the desired | ||
| resolution): | ||
| Maxent expects the n-s and e-w resolution to be the same. Following the | ||
| grass gis convention, the resolution of an exported raster is | ||
| determined by the region settings. So make sure to set the resolution | ||
| of the region so that the n-s and e-w resolution match. To accomplish | ||
| this, you can use (replaced the *** for the desired resolution): | ||
|
|
||
| <div class="code"><pre> | ||
| g.region -a res=*** | ||
| </pre></div> | ||
|
|
||
| <p> | ||
| Alternatively, you can set the <i>-e flag</i>. This will run g.region | ||
| Alternatively, you can set the <b>-e flag</b>. This will run g.region | ||
| for you, adjusting the resolution so both the ns and ew resolutionn | ||
| match the smallest of the two, using nearest neighbor resampling. | ||
|
|
||
| <p> | ||
| This addon is a vector based alternative to <em>r.out.maxent_swd</em>. | ||
| This addon is a vector-based alternative to <em>r.out.maxent_swd</em>. | ||
| It can be more efficient with sparse data points. The main difference | ||
| is that with this addon you can have more than one sample point per | ||
| raster cell. points per raster cell. If this is not desired, use | ||
| r.out.maxent_swd. Another difference is the option to export the | ||
| predictor raster layers to a user-defined folder. This can be used in | ||
| Maxent, Maxnet addon for R or other software. | ||
| raster cell. But note that you can use the <b>-t</b> flag to thin the | ||
| point layer so that there is never more than 1 point per raster cell. | ||
| Another difference is the option to export the predictor raster layers | ||
| to a user-defined folder. This can be used in Maxent, Maxnet addon for | ||
| R or other software. | ||
|
|
||
| <h2>EXAMPLES</h2> | ||
|
|
||
| The examples below use a dataset that you can download <a | ||
| href="https://ecodiv.earth/share/reader_SDM/grassmaxent_sampledata.zip">from | ||
| here</a>. It includes <a href="">vector point layer</a> with | ||
| observation locations of the pale-throated sloth (<i>Bradypus | ||
| tridactylus</i>) from <a | ||
| href="https://doi.org/10.15468/dl.br8b4a">GBIF</a>, a number of bioclim | ||
| raster layers from <a | ||
| href="https://www.worldclim.org/data/worldclim21.html">WorldClim</a>, | ||
| the <a href="https://www.iucnredlist.org/species/3037/210442660">IUCN | ||
| RedList range map</a> of the species, and a boundary layer of the South | ||
| American countries from <a | ||
| href="https://www.naturalearthdata.com/downloads/50m-cultural-vectors/">NaturalEarth</a>. | ||
|
|
||
| <p> | ||
| The zip file contains a <a | ||
| href="https://grass.osgeo.org/grass-stable/manuals/grass_database.html#grass-locations">GRASS | ||
| location</a>. Unzip it and put it in a GRASS GIS database. Next, open | ||
| GRASS GIS and go to the mapset <i>southamerica</i>. Download the zip | ||
| file, and unzip it in a GRASS GIS database. | ||
|
|
||
| <div class="code"> | ||
| <pre> | ||
| v.maxent.swd -t species=Bradypus_tridactylus \ | ||
| evp_maps=bio02,bio03@southamerica,bio08,bio09,bio13,bio15,bio17 \ | ||
| evp_cat=sa_eco_l2 alias_cat=landuse nbgp=10000 \ | ||
| bgr_output=maxentinput/bgrd_swd.csv \ | ||
| species_output=maxentinput/spec_swd.csv \ | ||
| export_rasters=maxentinput/envlayers | ||
| </pre> | ||
| </div> | ||
|
|
||
| <p> | ||
| The output is a folder <i>maxentinput</i> with the SWD files | ||
| bgrd_swd.csv and spec_swd.csv and the accompanying proj files. The | ||
| latter provide information about the CRS, which might be useful if you | ||
| want to import the point layers in another software tools. In addition, | ||
| the example code creates the raster layers of the environmental layes | ||
| in ascii format in the folder <i>envlayers</i>. | ||
|
|
||
| <p> | ||
| The created data layers can be used as input for <a | ||
| href="http://biodiversityinformatics.amnh.org/open_source/maxent/">Maxent</a>. | ||
| Alternatively, you can use it as input for the <em>r.maxent.train</em> | ||
| addon, which provides a convenient wrapper for the <i>Maxent</i> | ||
| software. | ||
|
|
||
| <h2>SEE ALSO</h2> | ||
|
|
||
| <ul> | ||
| <li>MaxEnt 3.4.1 (<a | ||
| href="http://biodiversityinformatics.amnh.org/open_source/maxent/"> | ||
| http://biodiversityinformatics.amnh.org/open_source/maxent/</a>)</li> | ||
| <li><a href="r.out.maxent_swd.html">r.out.maxent_swd</a>, the original | ||
| implementation using species distribution data in raster format.</li> | ||
| <li><a href="r.maxent.lambdas.html">r.maxent.lambdas</a> addon to | ||
| compute raw or logistic prediction maps from MaxEnt lambdas files.</li> | ||
| <li><a href="r.maxent.train.html">r.maxent.train</a> addon to | ||
| create/train a Maxent model. The addon provides a wrapper to the | ||
| Maxent software.</li> | ||
|
|
||
| <li><a href="r.out.maxent_swd.html">r.out.maxent_swd</a>, an | ||
| alternative implementation of this addon, using species | ||
| distribution data in raster format.</li> | ||
|
|
||
| <li><a href="r.maxent.lambdas.html">r.maxent.lambdas</a> addon to | ||
| compute raw or logistic prediction maps from MaxEnt lambdas | ||
| files.</li> | ||
| </ul> | ||
|
|
||
| <h2>REFERENCES</h2> | ||
|
|
||
| <ul> | ||
| <li> Steven J. Phillips, Miroslav Dudík, Robert E. Schapire.A | ||
| <li>MaxEnt 3.4.1 (<a | ||
| href="http://biodiversityinformatics.amnh.org/open_source/maxent/"> | ||
| http://biodiversityinformatics.amnh.org/open_source/maxent</a>)</li> | ||
| <li> Steven J. Phillips, Miroslav Dudík, Robert E. Schapire. A | ||
| maximum entropy approach to species distribution modeling. In | ||
| Proceedings of the Twenty-First International Conference on Machine | ||
| Learning, pages 655-662, 2004.</li> | ||
| <li>Steven J. Phillips, Robert | ||
| P. Anderson, Robert E. Schapire. Maximum entropy modeling of | ||
| species geographic distributions. Ecological Modelling, | ||
| 190:231-259, 2006.</li> | ||
| <li>Jane Elith, Steven J. Phillips, Trevor | ||
| Hastie, Miroslav Dudík, Yung En Chee, Colin J. Yates. A statistical | ||
| explanation of MaxEnt for ecologists. Diversity and Distributions, | ||
| 17:43-57, 2011. </li> | ||
| <li>Steven J. Phillips, Robert P. Anderson, Robert E. Schapire. | ||
| Maximum entropy modeling of species geographic distributions. | ||
| Ecological Modelling, 190:231-259, 2006.</li> | ||
| <li>Jane Elith, Steven J. Phillips, Trevor Hastie, Miroslav Dudík, | ||
| Yung En Chee, Colin J. Yates. A statistical explanation of MaxEnt | ||
| for ecologists. Diversity and Distributions, 17:43-57, 2011. </li> | ||
| <li>GBIF.org (12 November 2023) GBIF Occurrence Download | ||
| https://doi.org/10.15468/dl.br8b4a </li> | ||
| </ul> | ||
|
|
||
| <h2>AUTHOR</h2> | ||
|
|
||
| Paulo van Breugel, paulo at ecodiv.earth | ||
|
|
||
| <p> | ||
| HAS green academy University of Applied Sciences<br> | ||
| <a | ||
| href="https://www.has.nl/en/research/professorships/innovative-bio-monitoring-professorship/">Innovative | ||
| Biomonitoring research group</a><br> | ||
| <a | ||
| href="https://www.has.nl/en/research/professorships/climate-robust-landscapes-professorship/">Climate-robust | ||
| Landscapes research group</a> | ||
|
|
Oops, something went wrong.